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Originally published as Genetics Published Articles Ahead of Print on September 30, 2004.
Genetics, Vol. 169, 495-501, January 2005, Copyright © 2005
doi:10.1534/genetics.104.034884
On the Evolution of Codon Volatility
Jianzhi Zhang1
Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109
1 Address for correspondence: Department of Ecology and Evolutionary Biology, University of Michigan, 3003 Natural Science Bldg., 830 N. University Ave., Ann Arbor, MI 48109.
E-mail: jianzhi{at}umich.edu
Volatility of a codon is defined as the probability that a random point mutation in the codon generates a nonsynonymous change. It has been proposed that higher-than-expected mean codon volatility of a gene indicates that positive selection for nonsynonymous changes has acted on the gene in the recent past. I show that strong frequency-dependent selection (minority advantage) in large populations can increase codon volatility slightly, whereas directional positive selection has no effect on volatility. Factors unrelated to positive selection, such as expression-related or GC-content-related codon usage bias, also affect volatility. These and other considerations suggest that codon volatility has only limited utility for detecting positive selection at the DNA sequence level.
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